106 lines
No EOL
3.2 KiB
Python
106 lines
No EOL
3.2 KiB
Python
"""Test the scan planning algorithms of the Microscope.
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As well as low level function by function tests, this test suite also provides tests
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that simulate scanning a sample, checking that the expected path is followed.
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"""
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import re
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import pytest
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from pydantic import BaseModel
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import numpy as np
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# Just for testing importing as
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from openflexure_microscope_server.background_detect import (
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MissingBackgroundData,
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BackgroundDetectorStatus,
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BackgroundDetectAlgorithm,
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ChannelDistributions,
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ColourChannelDetectSettings,
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ColourChannelDetectLUV
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)
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RNG = np.random.default_rng()
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IMG_SHAPE = (820, 616, 3)
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BG_COLOR = [220, 215, 217]
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PERC_REGEX = re.compile(r"(\d+\.+\d)+%")
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@pytest.fixture
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def background_image():
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image = np.ones(IMG_SHAPE, dtype=np.int16)
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image[:, :, 0] *= BG_COLOR[0]
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image[:, :, 1] *= BG_COLOR[1]
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image[:, :, 2] *= BG_COLOR[2]
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image += RNG.normal(scale=3, size=IMG_SHAPE).astype("int16")
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image[image < 0] = 0
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image[image > 255] = 255
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return image.astype("uint8")
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@pytest.fixture
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def sample_image(background_image):
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image = background_image.copy()
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x_cent = IMG_SHAPE[0]//2
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image[:x_cent,:,0] -= 180
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return image
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def test_bg_detect_base_class():
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"""Test the base class for background detect.
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If initialised as is it should raise not implemented error.
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"""
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with pytest.raises(NotImplementedError):
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BackgroundDetectAlgorithm()
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def test_partial_base_class(background_image):
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"""Create a partial class so to initialise the base class and test other methods.
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This test is to check that if the necessary methods are not set, that an
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appropriate error is raise.
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"""
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class BadAlgo1(BackgroundDetectAlgorithm):
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"""Only has a settings model so it can initialise."""
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settings_data_model: BaseModel = ColourChannelDetectSettings
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bad_algo1 = BadAlgo1()
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status = bad_algo1.status
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assert not status.ready
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assert isinstance(status.settings, ColourChannelDetectSettings)
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with pytest.raises(NotImplementedError):
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# Should error on any dictionary input. This simulates loading settings from
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# disk
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bad_algo1.background_data = {"key": 1}
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with pytest.raises(NotImplementedError):
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bad_algo1.set_background(background_image)
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with pytest.raises(NotImplementedError):
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bad_algo1.image_is_sample(background_image)
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def test_colour_channel_luv(background_image, sample_image):
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cc_luv = ColourChannelDetectLUV()
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# No background data so it is not ready and will error if image_is_sample is called.
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assert not cc_luv.status.ready
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with pytest.raises(MissingBackgroundData):
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cc_luv.image_is_sample(background_image)
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# Set the background
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cc_luv.set_background(background_image)
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# Now it is ready
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assert cc_luv.status.ready
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sample, message = cc_luv.image_is_sample(background_image)
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assert not sample
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assert "0.0%" in message
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sample, message = cc_luv.image_is_sample(sample_image)
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assert sample
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match = PERC_REGEX.search(message)
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assert match is not None
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# Should be 50% background. Allowing 49.8-50.2% due to noise.
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assert 49.8 < float(match.group(1)) < 50.2
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# TODO Save data and reload it. |